Are there any benefits to running Subversion server on Linux as opposed to Windows?
We original ran Collabnet on Windows for around 12 months, and then we switched it to a Linux SVN system. Then, we split the repositories onto two seperate systems - one runs Ubuntu and one runs Windows Server 2003 R2.
There is absolutally no difference between them, they both run Active Directory integration brilliantly, they're both VM's and are just as fast as eachother, and none of our users have ever had an issue with either system.
So go with the OS you know the best.
One difference would be that a base OS for Ubuntu will most likely need less memory/storage when compared to a 2008r2 system. If don't need a vendor support then your Linux license will cost less compared to Windows.
But if you are not already familiar with maintaining a Linux box then you can easily eat up any of the savings from hardware and licence costs in support it on Linux.